Quick RPKM?

[AdrianP]

Hello,

I have a classic scenario where i have a bunch of predicted genes, and RNA-Seq data. I want RPKM for each gene, and I have the genes in a fasta file.

Suppose I align the reads to the genes using bowtie. What next? Any script to determine RPKM for each gene and sort the genes by RPKM values?

Thank you,
Adrian

[ThePresident]

I used bowtie to align my reads and cufflinks to extract RPKM values...

[AdrianP]

Would you mind sharing your command line to do that? Given any .bam file.

[ThePresident]

Oh my... It's been a while and I can't remember exactly and to be honest, I'm in the middle of an analysis. However, you'll find a manual here: cufflinks.cbcb.umd.edu/manual.html

TP

[a_mt]

Hi Adrian,

There's a qucik way to do it:

1. convert your SAM/BAM to wiggle file (you can use bedtools or check this)

2. multiply every value in wiggle by (1,000,000/no. of reads)

for eg: if you have 150 million reads, (1,000,000/150,000,000) would be 0.006666

So multiply every wiggle by 0.00666 !

Source: I read about this a long back on a blog. I dont remember the link though :P